QCeltis
QCeltis
Welcome to your QCeltis Quality Control Analysis Report! We are pleased to present to you a visual QC summary of your dataset. Representing high-dimensional omics data using plots helps us view large amounts of information at once to identifying patterns and trends across your samples and datasets. The QCeltis package monitors metrics based on the input datasets provided. For any concerns about or suggestions to improve this report, let the team know at GroupHeartBioinformaticsSupport@cshs.org, and we will consider your feedback. We are happy to support your computational needs.
The report is divided into 2 tabs:
The following ID-Free metrics have been extracted from the provided mzML files. Given thresholds have been applied and outlier analysis has been performed. If no outliers were found, outlier plots will not be plotted. If a grouping file was provided, additional groupwise plots will be included.
The total ion current (TIC) is the summed intensity across the entire range of masses being detected in each sample. MS1 and MS2 Total Ion Current Values extracted from spectra within the given mzML files
MS1 TIC is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition and LC-MS instrument performance such as improper autosampler sample pickup. Please check the specific samples listed below.
3 outliers were found. The following files have been detected as outliers: 20211018_Seroconversion_DBS_Plate1_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate6_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate8_DR2_centroid.mzML
MS2 TIC is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition and LC-MS instrument performance such as improper autosampler sample pickup. Please check the specific samples listed below.
3 outliers were found. The following files have been detected as outliers: 20211018_Seroconversion_DBS_Plate1_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate6_DR4_centroid.mzML, 20211018_Seroconversion_DBS_Plate8_DR2_centroid.mzML
When a grouping file is provided, CV% for TIC values across samples in each group is calculated. This provides an insignt into how consistent the samples are within each group.
CV% for MS1 TIC was calculated using TIC values from each sample within a provided group. All groups have passed the CV Threshold
CV% for MS2 TIC was calculated using TIC values from each sample within a provided group. All groups have passed the CV Threshold
The number of spectra recorded in each mzML file is extracted. The spectral ratio represents the number of MS2 Spectra over the number of MS1 Spectra found in each file.
The base peak intensity is the recorded intensity of the most intense peak from each spectrum in the mzML file. The Max Base Peak Intensity represents the highest recorded base peak intensity in each mzML file.
Max Base Peak Intensity is expected to be consistent across replicate quality control samples. Any outliers detected are highlighted in yellow. Outliers detected could point to issues with data acquisition or instrument performance such as sample pickup or samples being dried out. Please check the specific samples listed below.
1 outliers were found. The following files have been detected as outliers: 20211018_Seroconversion_DBS_Plate1_DR3_centroid.mzML
The following ID-Based metrics have been calculated and derived from the input search results that were provided. Given input thresholds have been applied and if grouping file was provided, additional groupwise plots will be included.
Number of proteins identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation, digestion protocols or experimental reproducibility.
Number of precursors identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation, digestion protocols or experimental reproducibility.
Cumulative Frequency % of calculated CV% of intensity values across all samples. This reveals the degree of variability across the dataset, higher CVs indicate greater variation that could be stemming from sample preparation, data acquisition or instrument performance. Lower CVs indicate higher reproducibility of protein, peptide or precursor intensities across replicate samples.
Intensity CV% across samples within each group is calculated. Threshold is set to 70.0% of proteins under 40.0 CV%. This provides information about the consistency and reproducibility of intensity values within each provided group. Any groups not meeting the threshold indicate batch or plate-specific issues that need to be looked into.
Intensity CV% across samples within each group is calculated. Threshold is set to 70.0% of precursors under 40.0 CV%. This provides information about the consistency and reproducibility of intensity values within each provided group. Any groups not meeting the threshold indicate batch or plate-specific issues that need to be looked into.
PCA plot from protein intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.
PCA plot from precursor intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.
The Total Ion Current here is calculated from intensities of common precursors found in all samples. Any inconsistent patterns could indicate problems in sample preparation.
Common Precursor TIC CV% calculated from intensities of common precursors within each provided group. A CV% higher than the set threshold of 40.0 indicates an inconsistency within the samples of the group.
Total Number of 0 miscleaved peptides found in each sample. If the percentage of 0 miscleaved peptides is under the miscleavage threshold value of 60.0%, this could indicate issues with sample preparation and digestion protocols.